loadTransitonsMSExperiment: load msexperiment with nrt transtions and peptides

In wolski/imsbInfer: Visualization, normalization and QC of proteomics SWATH-MS data

Description

Selects top nrt transitions based on median transition intensity in all runs. Selects top nr peptides based on median peptide intensity in all runs.

Usage

loadTransitonsMSExperiment(obj, nrt = 3, peptop = 3)

Arguments

obj	a table produced by feature alignment
nrt	number of transitions
peptop	nr of top peptides

Examples

library(imsbInfer)
data( feature_alignment_requant )

#SpecLib = ("C:/Users/witek/Google Drive/DataAnalysis/EBhardt/data/E1404301658-sample-SpecLib/feature_alignment_requant.tsv")
#SpecLib = ("/media/witold/data/googledrive/DataAnalysis/EBhardt/data/E1404301658-sample-SpecLib/feature_alignment_requant.tsv")
#obj  = fread(SpecLib)
#nrt = 3
#peptop = 3
#obj =feature_alignment_requant
x = loadTransitonsMSExperiment( feature_alignment_requant , nrt= 3, peptop=3)
x = loadTransitonsMSExperiment( feature_alignment_requant )
table(table(feature_alignment_requant$transition_group_id))
table(table(x$pepinfo$transition_group_id))
x2 = loadTransitonsMSExperiment(feature_alignment_requant, nrt= 20, peptop=20)
table(table(x2$pepinfo$ProteinName))
table(table(x2$pepinfo$PeptideSequence))
dim(x)
head(x$pepinfo)
mypairs(x$Intensity[,1:3])
#check that ordering is consistent
xx = split2table(rownames(x$pepinfo),split="-")
stopifnot(xx[,1] == x$pepinfo$transition_group_id)
stopifnot(xx[,2] == x$pepinfo$aggr_Fragment_Annotation)

wolski/imsbInfer documentation built on March 27, 2021, 11:39 p.m.